Table of features, taxons and samples

[buzic (Victoria)]

Hello,
I’m using qiime2-2023.5 installed via conda. I am attempting to extract some information from my Qiime2 artifacts. What I need is a similar to information I already have from the rep-seq, taxonomy and table visualizations but with added details in samples column.

At the moment I have the table visualization created by:

qiime feature-table summarize \
--i-table cd_16s_table.qza \
--o-visualization cd_16s_table-viz.qzv \
--m-sample-metadata-file cd_16_metadata.tsv

Which gives me this :

And the table of taxonomy and rep-sequences created by the command:

qiime metadata tabulate \
--m-input-file cd_16s_taxonomy_results.qza \
--m-input-file cd_16s_rep-seqs.qza \
--o-visualization cd_16s-combined-feature-rep-tax.qzv

Which results in this:

What I would like is a something with four columns: Feature-ID, Sequence, taxon, Samples observed in. Where ‘Samples observed in’ is not a number but a list of the sample names it is found in. So the table I need would look like the following:

A similar question was asked here and someone mentions using sample-id instead of features-id as an index – however I would like to retain feature-ID.

Many thanks

[cherman2 (Chloe Herman)]

Hi @buzic,
QIIME feature-table tabulate-seqs will get you feature-id, sequences, and taxon in one table. You will need to pass in your rep-seqs and your taxonomy.

QIIME feature-table tabulate-seqs can add metadata as well so if you had metadata that had the 'samples observed in' info QIIME feature-table tabulate-seqs could create this table

Unfortunately, there is not an easy way to create 'samples observed in' list metadata in QIIME 2. This might be something you could do in R or in python.
I hope that helps!

[buzic (Victoria)]

Thanks very much. Just incase anyone else finds this and needs some other format or to extract which samples had which ASV's, I actually decided to export my taxonomy and table information:

qiime tools export \
--input-path cd_16s_table.qza \
--output-path cd_16s_table-export

qiime tools export \
--input-path cd_16s_taxonomy_results.qza \
--output-path cd_16s_taxonomy_results-export

then convert the feature table, as it's in biom format:

cd cd_16s_table-export
biom convert -i feature-table.biom -o feature-table.tsv --to-tsv

I'm writing a python code to merge the formats on Feature ID. I'll just keep the per sample read out from the feature-table.tsv (much more sensible!). So my table will eventually have the columns Feature-ID, Sequence, Taxonomy, SampleA, SampleB, SampleC.... etc. Where the sample columns contain the number of times that ASV was found in that sample.

cheers,

Vic